I agree with the people before me - the assumption that killing Lupi and Co. somehow alters drop rates is baseless superstition, and with drop rates as ridiculously low as they are, it's virtually impossible to prove anything one way or the other. It would take thousands of runs to make any sort of statement of statistical significance about it.

What I can tell you is that I've done more SF runs than I care to remember - solo runs, team runs, heck, I even solo'd a team run - but I've never seen a unique drop.
I almost never kill Lupi and friends in my runs. Not because of the superstition, mind you, but rather because they don't attack me, and I therefore couldn't be bothered to waste a chakra-filled bullet on them.

I agree though.
I think people, myself sometimes included, only believe that not killing or killing the fluttery blue crew will effect drop rates is cause it seems kind of hopeless that you'll ever pick up a unique a LOT of the time. So it's just kinda nice to have a little bit of extra hope even if it comes from something that's kind of silly and superstitious.